Installation

Requirements

In order to use SBpipe, the following packages must be installed:

Please, make sure that Python pip and Rscript work fine. SBpipe can work with the simulators:

  • COPASI 4.19+ - http://copasi.org/ (for model simulation, parameter scan, and parameter estimation)
  • Python (directly or as a wrapper to call models coded in any programming language)

If LaTeX/PDF reports are also desired, the following package must also be installed:

  • LaTeX 2013+

Installation on GNU/Linux

Installation of COPASI

As of 2016, COPASI is not available as a package in GNU/Linux distributions. Users must add the path to COPASI binary files manually editing the GNU/Linux $HOME/.bashrc file as follows:

# Path to CopasiSE (update this accordingly)
export PATH=$PATH:/path/to/CopasiSE/

The correct installation of CopasiSE can be tested with:

# Reload the .bashrc file
source $HOME/.bashrc

CopasiSE -h
> COPASI 4.19 (Build 140)

Installation of LaTeX

Users are recommended to install LaTeX/texlive using the package manager of their GNU/Linux distribution. On GNU/Linux Ubuntu machines the following package is required:

texlive-latex-base

The correct installation of LaTeX can be tested with:

pdflatex -v
> pdfTeX 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian)
> kpathsea version 6.2.1
> Copyright 2015 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).

Installation of SBpipe via Python pip

SBpipe and its Python dependencies can simply be installed via Python pip using the command:

# install sbpipe from pypi.org via pip
pip install sbpipe

In order to analyse the data, SBpipe requires the R package sbpiper, which can be installed as follows:

# install sbpiper from r-cran
Rscript -e "install.packages('sbpiper', dep=TRUE, repos='http://cran.r-project.org')"

Installation of SBpipe via Conda

Users need to download and install Miniconda3 (https://conda.io/miniconda.html). SBpipe will be installed in a dedicated conda environment:

# create a new environment `sbpipe`
conda create -n sbpipe

# activate the environment.
# For old versions of conda, replace `conda` with `source`.
conda activate sbpipe

# install sbpipe and its dependencies (including sbpiper)
conda install -c bioconda sbpipe

Installation of SBpipe from source

Users need to install git.

# clone SBpipe from GitHub
git clone https://github.com/pdp10/sbpipe.git
# move to sbpipe folder
cd sbpipe
# install SBpipe dependencies on GNU/Linux, run:
make

Finally, to run sbpipe from any shell, users need to add ‘sbpipe/scripts’ to the PATH environment variable by adding the following lines to the $HOME/.bashrc file:

# SBPIPE (update this accordingly)
export PATH=$PATH:/path/to/sbpipe/scripts

The .bashrc file should be reloaded to apply the previous edits:

# Reload the .bashrc file
source $HOME/.bashrc

Installation on Windows

See installation on GNU/Linux and install SBpipe via PIP or Conda. Windows users need to install LaTeX MikTeX https://miktex.org/.

Testing SBpipe

The correct installation of SBpipe and its dependencies can be verified by running the following commands. For the correct execution of all tests, LaTeX must be installed.

# SBpipe version:
sbpipe -V
> sbpipe 4.13.0

Unless SBpipe was installed from source, users need to download the source code at the page https://github.com/pdp10/sbpipe/releases to run the test suites.

# unzip and change path
unzip sbpipe-X.Y.Z.zip
cd sbpipe-X.Y.Z/tests

# run model simulation using COPASI (see results in tests/copasi_models):
nosetests test_copasi_sim.py --nocapture

# run all tests:
nosetests test_suite.py --nocapture

# generate the manuscript figures (see results in tests/insulin_receptor):
nosetests test_suite_manuscript.py --nocapture